fix flattening time-point specific override failures

[yannikschaelte]

fixes #363

[codecov]

Codecov Report

Merging #404 into develop will decrease coverage by 0.05%.
The diff coverage is 75%.

@@             Coverage Diff             @@
##           develop     #404      +/-   ##
===========================================
- Coverage    77.84%   77.78%   -0.06%     
===========================================
  Files           22       22              
  Lines         2072     2098      +26     
  Branches       476      486      +10     
===========================================
+ Hits          1613     1632      +19     
- Misses         340      343       +3     
- Partials       119      123       +4

Impacted Files	Coverage Δ
petab/core.py	82.23% <75%> (-1.9%)	⬇️

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[dweindl]

Looks good to me. @LeonardSchmiester please check that the issues you had are resolved.

[LeonardSchmiester]

For the Sobotta model I get:

Traceback (most recent call last):
  File "/home/leonard/Anaconda/envs/benchmark_collection/lib/python3.7/site-packages/IPython/core/interactiveshell.py", line 3319, in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)
  File "<ipython-input-5-73ba67d08c8d>", line 1, in <module>
    flatten_petab_problem = flatten_timepoint_specific_output_overrides(petab_problem)
  File "/home/leonard/Anaconda/envs/benchmark_collection/lib/python3.7/site-packages/petab/core.py", line 178, in flatten_timepoint_specific_output_overrides
    df[OBSERVABLE_PARAMETERS].str.find(cur_sc)
  File "/home/leonard/Anaconda/envs/benchmark_collection/lib/python3.7/site-packages/pandas/core/strings.py", line 1954, in wrapper
    return func(self, *args, **kwargs)
  File "/home/leonard/Anaconda/envs/benchmark_collection/lib/python3.7/site-packages/pandas/core/strings.py", line 3083, in find
    result = str_find(self._parent, sub, start=start, end=end, side="left")
  File "/home/leonard/Anaconda/envs/benchmark_collection/lib/python3.7/site-packages/pandas/core/strings.py", line 1366, in str_find
    raise TypeError(msg)
TypeError: expected a string object, not float

Possibly due to some empty observableParameter / noiseParameter rows.

Additionally I think the function will still scale very badly with the size of the measurement file. Why do we need the <= in lines 159 & 161? Shouldn't == do the job?

[LeonardSchmiester]

Well, it doesn't throw an error anymore. But the ouput is a nonType object which I guess is not intended!? Might be the same reason as in my comment in #363?